Ahmed,
We are not exactly sure what is causing your issue. We would like a schematic to better understand your system. It is important to note that the inputs to the LM628 should be in quadrature for correct counting. What is the input to the LM628 when the extensometer is used? We think what may be happening is that there are timing issues between what the LM628 receives at the input signals and internal clock so that some pulses are being counted and some aren't. What is the timing of the spurious pulses and what clock speeds have you tried? You might want to slow the clock down to possibly miss more of the random spurious pulses. I will continue to look into this issue but please provide a system schematic.